[yt-users] scipy broke yt? maybe python?

[Nathan Goldbaum]

On Fri, Jul 1, 2016 at 4:37 PM, Stephanie Tonnesen <stonnes at gmail.com>
wrote:

> Hi Nathan,
>
> Yahoo!  doing the conda install instead of pip has fixed it!
>

The 4th of July weekend is saved!


> For completion, though, here are the answers to the other two questions:
>
> Yes, it all runs nicely (until scipy is needed) if I don't have scipy
> installed.
>
> If I start python and type
>
> import scipy.optimize
>
> I get a Segmentation fault --when I used the pip install version.  with
> conda install, import scipy.optimize seems to work fine.
>

This must be a bug in scipy then, triggered by pip installing in whatever
environment you have set up on this cluster.


> Thanks!!!
> Stephanie
>
>
> --
> Dr. Stephanie Tonnesen
> Alvin E. Nashman Postdoctoral Fellow
> Carnegie Observatories, Pasadena, CA
> stonnes at gmail.com
>
> On Fri, Jul 1, 2016 at 2:15 PM, Nathan Goldbaum <nathan12343 at gmail.com>
> wrote:
>
>>
>> On Fri, Jul 1, 2016 at 4:00 PM, Stephanie Tonnesen <stonnes at gmail.com>
>> wrote:
>>
>>> Hi Nathan,
>>>
>>> I am not sure how to get a core dump or how to make gdb give me useful
>>> things.  But maybe this will help...
>>>
>>> By running my code via a command line, I find that
>>> import h5py
>>> import scipy
>>> import yt
>>> from yt.analysis_modules.cosmological_observation.api import LightRay
>>>
>>> all are fine.  But,
>>>
>>> from yt.analysis.modules.absorption_spectrum.api import
>>> AbsorptionSpectrum
>>> from yt.analysis.modules.absorption_spectrum.api import
>>> generate_total_fit
>>>
>>
>> And both of these succeed when scipy isn't installed?
>>
>> What happens if you do:
>>
>> import scipy.optimize
>>
>> Also you're using the conda-based python that the latest version of the
>> install script builds, right? Maybe you should try the conda binary builds
>> instead:
>>
>> $ pip uninstall scipy
>> $ conda install scipy
>>
>>
>>>
>>> both give me a Segmentation fault and kick me out of python
>>>
>>> I can keep trying to figure out how to have gdb give me something
>>> useful, but does this give any clues in the meantime?
>>>
>>> Thanks,
>>> Stephanie
>>>
>>> --
>>> Dr. Stephanie Tonnesen
>>> Alvin E. Nashman Postdoctoral Fellow
>>> Carnegie Observatories, Pasadena, CA
>>> stonnes at gmail.com
>>>
>>> On Fri, Jul 1, 2016 at 12:28 PM, Nathan Goldbaum <nathan12343 at gmail.com>
>>> wrote:
>>>
>>>> Hi Stephanie,
>>>>
>>>> It's very hard to say what's going wrong without more information.
>>>>
>>>> Can you get a core dump or run python under gdb to get a stack trace at
>>>> the place where the segmentation fault happens?
>>>>
>>>> Can you run this on your laptop? If so, do you get a segmentation fault
>>>> there?
>>>>
>>>> -Nathan
>>>>
>>>> On Fri, Jul 1, 2016 at 2:25 PM, Stephanie Tonnesen <stonnes at gmail.com>
>>>> wrote:
>>>>
>>>>> Hi all,
>>>>>
>>>>> I have the yt-conda installation of yt.  I am trying to create an
>>>>> absorption spectrum, so need the command "generate_total_fit".
>>>>>
>>>>> yt told me I needed scipy for this to work.  yt does not have scipy.
>>>>> So I typed:
>>>>> >pip install scipy
>>>>>
>>>>> scipy was installed.
>>>>>
>>>>> However, then my submission script no longer worked at all and I was
>>>>> given the error:
>>>>>
>>>>> /var/spool/torque/mom_priv/jobs/50052.mies.stanford.edu.SC: line 26:
>>>>> 3750 Segmentation fault      python HI_absorbers.py
>>>>>
>>>>> When I pip uninstall scipy, my code runs again!
>>>>> The only commands in my script are
>>>>> source /home/stonnes/yt-conda/bin/activate
>>>>> python HI_absorbers.py
>>>>>
>>>>> Can anyone help me out with this?
>>>>>
>>>>> Thanks!
>>>>> Stephanie
>>>>>
>>>>> --
>>>>> Dr. Stephanie Tonnesen
>>>>> Alvin E. Nashman Postdoctoral Fellow
>>>>> Carnegie Observatories, Pasadena, CA
>>>>> stonnes at gmail.com
>>>>>
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>>>>>
>>>>>
>>>>
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